Swiss Social Democratic MP Evi Allemann claims that Saab has been quietly financing campaigners in favour of the deal, worth an estimated 3.1 billion Swiss francs ($3.47 billion).
While Saab's support of the pro-Gripen campaign may not be technically illegal, Allemann sees the Swedish firm's behaviour as bordering on scandalous.
"We don't have any clear rules for referendum campaigns, as a result, foreign companies feel they can shamelessly get involved in national decisions," she told the TT news agency.
Saab has neither confirmed nor denied the accusations, citing Swiss rules which "also include refraining from comment on campaign financing".
But the accusations of Saab's involvement has also caused concern among those who support the deal, with the leader of the liberal FDP party, Philpp Müller, calling such actions "counterproductive".
"It makes it harder for us centre-right politicians to convince people of the importance of the Gripen purchase," Müller told Swiss newspaper Blick.
The developments come following a decision taken last week that a referendum on the deal would be held on May 18th. Opponents submitted over 100,000 signatures seeking a referendum, with campaigners hoping to block the Gripen deal.
Under Switzerland's system of direct democracy, citizens can have the last word on a huge array of issues if campaigners muster enough signatures from voters in order to force a plebiscite.
Polls have shown that a majority of voters oppose the Gripen deal.
Approved by the government in 2011 and backed by parliament last year, it cannot be blocked as such.
But opponents have been able to contest the law that allows the purchase to be funded by drawing an annual 300 million Swiss francs from the army's budget over 10 years.
The coalition campaigning against the deal is steered by the left-leaning Socialists and Greens, as well as anti-militarists, but also includes economic liberals opposed to the price tag.
The opponents also argue that the model of Gripen chosen by the authorities only exists on paper, as its maker, Sweden's Saab, is still developing it.
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Last month, Saab's Gripen beat the Rafale, made by France's Dassault, and the F/A 18 Super Hornet built by US company McDonnell Douglas in the race to sell 36 planes to Brazil.
The estimated value of the Brazil deal is $5 billion.
The air force of neutral Switzerland currently has 32 Super Hornets in service, purchased in 1996.
There are currently 166 Gripen fighters in service globally, with 100 in Sweden, 26 in South Africa, 14 each in the Czech Republic and Hungary, and 12 in Thailand, according to Saab.